The data, obtained by Gannett’s Albany Bureau, showed that the number of employees making more than $200,000 increased 37 percent, from 689 to 944 workers.

The higher salaries come as Gov. Andrew Cuomo has limited state employment and frozen union salaries, and state officials said many of the top earners are outside his purview.

The number of state workers earning more than $100,000 increased from about 24,000 to 27,000 since 2011, the records from the state Comptroller’s Office showed.

Fifteen of the top 20 state salaries in 2012 worked at SUNY Downstate Medical Center, the financially strapped Brooklyn facility that was criticized for mismanagement in a comptroller’s audit last month.

The top earner in the state was Antonio Alfonso, a professor at the center and its head of surgery. He earned nearly $1.1 million last year through his various roles. He ranked second in 2011 at $776,000.

About Capitol Confidential

Capitol Confidential gathers the best coverage of New York politics and puts it all together. Each section - Capitol, The State Worker, New York on the Potomac, and Voices - represents a unique facet of the political scene. The Capitol section features coverage from the Times Union Capitol bureau. The State Worker is dedicated to state worker issues. New York on the Potomac offers news of interest to New Yorkers from Washington. And Voices features the best of everything else, pointing you to columnists and bloggers from across the Web.